Warning

This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for tool_shed.webapp.model.migrate.versions.0016_add_do_not_test_tools_functionally_correct_errors_columns

"""
Migration script to add the tool_test_errors, do_not_test, tools_functionally_correct, and time_last_tested columns to the repository_metadata table.
"""

import logging
import sys

from sqlalchemy import Boolean, Column, DateTime, MetaData, Table

# Need our custom types, but don't import anything else from model
from galaxy.model.custom_types import JSONType

log = logging.getLogger(__name__)
log.setLevel(logging.DEBUG)
handler = logging.StreamHandler(sys.stdout)
format = "%(name)s %(levelname)s %(asctime)s %(message)s"
formatter = logging.Formatter(format)
handler.setFormatter(formatter)
log.addHandler(handler)

metadata = MetaData()


[docs]def upgrade(migrate_engine): print(__doc__) metadata.bind = migrate_engine metadata.reflect() # Create and initialize tools_functionally_correct, do_not_test, time_last_tested, and tool_test_errors columns in repository_metadata table. RepositoryMetadata_table = Table("repository_metadata", metadata, autoload=True) c = Column("tools_functionally_correct", Boolean, default=False, index=True) try: # Create tools_functionally_correct column c.create(RepositoryMetadata_table, index_name="ix_repository_metadata_tfc") assert c is RepositoryMetadata_table.c.tools_functionally_correct # Initialize. if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite': default_false = "0" elif migrate_engine.name in ['postgresql', 'postgres']: default_false = "false" migrate_engine.execute("UPDATE repository_metadata SET tools_functionally_correct=%s" % default_false) except Exception: log.exception("Adding tools_functionally_correct column to the repository_metadata table failed.") c = Column("do_not_test", Boolean, default=False, index=True) try: # Create do_not_test column c.create(RepositoryMetadata_table, index_name="ix_repository_metadata_dnt") assert c is RepositoryMetadata_table.c.do_not_test # Initialize. if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite': default_false = "0" elif migrate_engine.name in ['postgresql', 'postgres']: default_false = "false" migrate_engine.execute("UPDATE repository_metadata SET do_not_test=%s" % default_false) except Exception: log.exception("Adding do_not_test column to the repository_metadata table failed.") c = Column("time_last_tested", DateTime, default=None, nullable=True) try: # Create time_last_tested column c.create(RepositoryMetadata_table, index_name="ix_repository_metadata_tlt") assert c is RepositoryMetadata_table.c.time_last_tested except Exception: log.exception("Adding time_last_tested column to the repository_metadata table failed.") c = Column("tool_test_errors", JSONType, nullable=True) try: # Create tool_test_errors column c.create(RepositoryMetadata_table, index_name="ix_repository_metadata_tte") assert c is RepositoryMetadata_table.c.tool_test_errors except Exception: log.exception("Adding tool_test_errors column to the repository_metadata table failed.")
[docs]def downgrade(migrate_engine): metadata.bind = migrate_engine metadata.reflect() # Drop tool_test_errors, time_last_tested, do_not_test, and tools_functionally_correct columns from repository_metadata table. RepositoryMetadata_table = Table("repository_metadata", metadata, autoload=True) try: RepositoryMetadata_table.c.tool_test_errors.drop() except Exception: log.exception("Dropping column tool_test_errors from the repository_metadata table failed.") try: RepositoryMetadata_table.c.time_last_tested.drop() except Exception: log.exception("Dropping column time_last_tested from the repository_metadata table failed.") try: RepositoryMetadata_table.c.do_not_test.drop() except Exception: log.exception("Dropping column do_not_test from the repository_metadata table failed.") try: RepositoryMetadata_table.c.tools_functionally_correct.drop() except Exception: log.exception("Dropping column tools_functionally_correct from the repository_metadata table failed.")